drhchen

paper-qa

High accuracy RAG for answering questions from scientific documents with citations

HattCI

HattCI is a hidden Markov model for attC site identification in DNA sequence described in Pereira et al. 2016 (doi:10.1089/cmb.2016.0024)

PlasmidSeeker

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

Bacsort

a collection of scripts for organising bacterial genomes by species

mcorr

Inferring bacterial recombination rates from large-scale sequencing datasets.

Ecoli_database

Supplementary E. coli virulence associated genes, including etsABC, cdtABC (I, II, III, IV and V), papG (I, II and III), uclD, entA, sinH, f17b-A, f17b-G, clbS, plasmid-borne ompT, hlyF and mig14, pdu operon, capsule (K1, K2, K5, K14, K100) genes, mcmA, and stx subtypes.

mob-suite

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

spaTyper

Computational method for finding spa types.

staphopia-sccmec

Archived - please see updated sccmec tool at link below

RNASeq

Bacterial RNASeq analysis pipeline

kegg_enrich

kegg enrichment analysis

pharokka

fast phage annotation program

scripts

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

scripts

CNproScan

CNV detection for prokaryote genomes using NGS sequencing data

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

resequence

Bacterial variants(structural variant and single nucleotide variant) calling pipeline by short read NGS data

PaperBLAST

PaperBLAST: find papers about a protein or its homologs

staph_adaptation_paper

Scripts to analyse within-host evolution during S. aureus colonisation and infection

maskrc-svg

Masks recombination as detected by ClonalFrameML or Gubbins and draws an SVG

itol.toolkit

Helper Functions for Interactive Tree Of Life (iTOL)

table2itol

Generating iToL annotations from Spreadsheet or CSV files

coinfinder

A tool for the identification of coincident (associating and dissociating) genes in pangenomes.

amr_pangenome

Pan-genome construction/analysis tools centered around PATRIC and antimicrobial resistance

genomegaMap

Within-species genome-wide dN/dS estimation from very many genomes

Maaslin2

MaAsLin2: Microbiome Multivariate Association with Linear Models

staphylococcus-pseudintermedius

This repository contains all code used in Sawhney & Vargas et al. (2023).

pysradb

Package for fetching metadata and downloading data from SRA/ENA/GEO

Pactyper

Clone type prediction for WGS sequenced clinical bacterial isolates based on provided core genome.

reddog-nf

pipeline for read mapping, snp calling and annotation for bacterial genomes